This dataset contains biological, physical, and survey - biological data collected at lab UHawaii_SOEST during deployment Goetze_2012-2013 in the North Pacific Ocean from 2013-05-27 to 2013-06-05. These data include abundance, chlorophyll a, salinity calculated from CTD primary sensors, and water temperature. The instruments used to collect these data include Flow Meter, Microscope - Optical, Plankton Net, and qPCR Thermal Cycler. These data were collected by Erica Goetze of University of Hawaii at Manoa as part of the "New molecular methods for studying copepod nauplii in the field (EAGER: Copepod nauplii)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2021-01-20.
The following is the text of the dataset description provided by BCO-DMO:
Initial conditions and naupliar abundances of Parvocalanus crassirostris and Bestilina similis: MEPS 2017
Dataset Description:
Acquisition Description:
From Jungbluth et al. 2017 – MEPS:
Estimates of in situ naupliar abundance
Naupliar abundances of the 2 target species in situ were estimated using a quantitative polymerase chain reaction (qPCR)-based method (Jungbluth et al. 2013), as well as microscopic counts of calanoid and cyclopoid nauplii. The qPCR-based method allows application of individual species grazing rates to in situ abundances to estimate the total potential grazing impact of each species. Samples were collected by duplicate vertical microplankton net tows (0.5 m diameter ring net, 63 µm mesh) from near bottom (10 m depth) to the surface with a low speed flow meter (General Oceanics). The contents of each net were split quantitatively. One half was size-fractionated through a series of 5 Nitex sieves (63, 75, 80, 100, and 123 µm) to separate size groups of nauplii from later developmental stages, and each was preserved in 95% non-denatured ethyl alcohol (EtOH). The second half of the sample was preserved immediately in 95% EtOH for counts of total calanoid and total cyclopoid nauplii, which were used for comparison to the qPCR-based results of the abundance of each calanoid species. All samples were stored on ice in the field until being transferred to a -20°C freezer in the laboratory. EtOH in the sample bottles was replaced with fresh EtOH within 12 to 24 h of collection to ensure high-quality DNA for analysis (Bucklin 2000).
The 3 smallest plankton size fractions from the net collection were analyzed with qPCR to enumerate P. crassirostris and B. similis nauplius abundances (Jungbluth et al. 2013). In brief, DNA was extracted from 3 plankton size fractions (63, 75, and 80 µm) using a modified QIAamp Mini Kit procedure (Qiagen). The total number of DNA copies in each sample was then measured using species-specific DNA primers and qPCR protocols (Jungbluth et al. 2013). On each qPCR plate, 4 to 5 standards spanning 4 to 5 orders of magnitude in DNA copy number were run along with the 2 biological replicates of a size fraction for each sampling date along with a no template control (NTC), all in triplicate. A range of 0.04 to 1 ng µl-1 of total DNA per sample was measured on each plate ensuring that the range of standards encompassed the amplification range of samples, with equal total DNA concentrations run in each well on individual plates. In all cases, amplification efficiencies ranged from 92 to 102%, and melt-curves indicated amplification of only the target species. The qPCR estimate of each species' mitochondrial cytochrome oxidase c subunit I (COI) DNA copy number was converted to an estimate of nauplius abundance using methods described in Jungbluth et al. (2013).
Conditions
Salinity and temperature in the field were measured using a YSI 6600V2 sonde prior to collecting water for bottle incubations. For chl a, triplicate 305 ml samples were filtered onto GF/Fs (Whatman), flash-frozen (LN2), and kept at -80°C freezer until measurements were made 4 mo later. Chl a (and phaeopigment) was measured using a Turner Designs (model 10AU) fluorometer, using the standard extraction and acidification technique (Yentsch & Menzel 1963, Strickland & Parsons 1972).
For complete methodology, see the Supplemental Files section.
About this Dataset
| Title | Initial field conditions at Kane‘ohe Bay, Oahu, Hawaii and abundances of Parvocalanus crassirostris and Bestilina similis nauplii, May/June 2013 (EAGER: Copepod nauplii project) (NCEI Accession 0277882) |
|---|---|
| Description | This dataset contains biological, physical, and survey - biological data collected at lab UHawaii_SOEST during deployment Goetze_2012-2013 in the North Pacific Ocean from 2013-05-27 to 2013-06-05. These data include abundance, chlorophyll a, salinity calculated from CTD primary sensors, and water temperature. The instruments used to collect these data include Flow Meter, Microscope - Optical, Plankton Net, and qPCR Thermal Cycler. These data were collected by Erica Goetze of University of Hawaii at Manoa as part of the "New molecular methods for studying copepod nauplii in the field (EAGER: Copepod nauplii)" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2021-01-20. The following is the text of the dataset description provided by BCO-DMO: Initial conditions and naupliar abundances of Parvocalanus crassirostris and Bestilina similis: MEPS 2017 Dataset Description: Acquisition Description: From Jungbluth et al. 2017 – MEPS: Estimates of in situ naupliar abundance Naupliar abundances of the 2 target species in situ were estimated using a quantitative polymerase chain reaction (qPCR)-based method (Jungbluth et al. 2013), as well as microscopic counts of calanoid and cyclopoid nauplii. The qPCR-based method allows application of individual species grazing rates to in situ abundances to estimate the total potential grazing impact of each species. Samples were collected by duplicate vertical microplankton net tows (0.5 m diameter ring net, 63 µm mesh) from near bottom (10 m depth) to the surface with a low speed flow meter (General Oceanics). The contents of each net were split quantitatively. One half was size-fractionated through a series of 5 Nitex sieves (63, 75, 80, 100, and 123 µm) to separate size groups of nauplii from later developmental stages, and each was preserved in 95% non-denatured ethyl alcohol (EtOH). The second half of the sample was preserved immediately in 95% EtOH for counts of total calanoid and total cyclopoid nauplii, which were used for comparison to the qPCR-based results of the abundance of each calanoid species. All samples were stored on ice in the field until being transferred to a -20°C freezer in the laboratory. EtOH in the sample bottles was replaced with fresh EtOH within 12 to 24 h of collection to ensure high-quality DNA for analysis (Bucklin 2000). The 3 smallest plankton size fractions from the net collection were analyzed with qPCR to enumerate P. crassirostris and B. similis nauplius abundances (Jungbluth et al. 2013). In brief, DNA was extracted from 3 plankton size fractions (63, 75, and 80 µm) using a modified QIAamp Mini Kit procedure (Qiagen). The total number of DNA copies in each sample was then measured using species-specific DNA primers and qPCR protocols (Jungbluth et al. 2013). On each qPCR plate, 4 to 5 standards spanning 4 to 5 orders of magnitude in DNA copy number were run along with the 2 biological replicates of a size fraction for each sampling date along with a no template control (NTC), all in triplicate. A range of 0.04 to 1 ng µl-1 of total DNA per sample was measured on each plate ensuring that the range of standards encompassed the amplification range of samples, with equal total DNA concentrations run in each well on individual plates. In all cases, amplification efficiencies ranged from 92 to 102%, and melt-curves indicated amplification of only the target species. The qPCR estimate of each species' mitochondrial cytochrome oxidase c subunit I (COI) DNA copy number was converted to an estimate of nauplius abundance using methods described in Jungbluth et al. (2013). Conditions Salinity and temperature in the field were measured using a YSI 6600V2 sonde prior to collecting water for bottle incubations. For chl a, triplicate 305 ml samples were filtered onto GF/Fs (Whatman), flash-frozen (LN2), and kept at -80°C freezer until measurements were made 4 mo later. Chl a (and phaeopigment) was measured using a Turner Designs (model 10AU) fluorometer, using the standard extraction and acidification technique (Yentsch & Menzel 1963, Strickland & Parsons 1972). For complete methodology, see the Supplemental Files section. |
| Modified | 2023-05-05T11:47:48.134Z |
| Publisher Name | N/A |
| Contact | N/A |
| Keywords | 0277882 , CHLOROPHYLL A , SALINITY , species abundance , WATER TEMPERATURE , flow meter , microscope , net - plankton net , biological , physical , survey - biological , University of Hawai'i at Mānoa , Biological and Chemical Oceanography Data Management Office , Kaneohe Bay , North Pacific Ocean , oceanography , BCO-DMO > Biological and Chemical Oceanography Data Management Office , New molecular methods for studying copepod nauplii in the field (EAGER: Copepod nauplii) , Goetze_2012-2013 , Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1255697 , abundance , chlorophyll a , experiment id , latitude , longitude , no standard parameter , salinity calculated from CTD primary sensors , water temperature , EARTH SCIENCE > OCEANS > OCEAN CHEMISTRY > CHLOROPHYLL , EARTH SCIENCE > OCEANS > OCEAN TEMPERATURE > WATER TEMPERATURE , EARTH SCIENCE > OCEANS > SALINITY/DENSITY > SALINITY , chl_a , chl_std_err , counted_total_nauplii , counted_total_nauplii_se , date_local , experiment , lat , lon , qPCR_Bestiolina , qPCR_Bestiolina_se , qPCR_Parvocalanus , qPCR_Parvocalanus_se , sal , temp , Flow Meter , Microscope - Optical , Plankton Net , qPCR Thermal Cycler , MICROSCOPES > MICROSCOPES , PLANKTON NETS , General Oceanics Digital Flowmeter , Roche LC96 thermalcycler , microplankton net , unknown (Microscope - Optical) , lab UHawaii_SOEST , LABORATORY > LABORATORY , OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS , OCEAN > PACIFIC OCEAN > NORTH PACIFIC OCEAN , Kaneohe Bay, HI , environment , oceans , biota |
{
"identifier": "gov.noaa.nodc:0277882",
"accessLevel": "public",
"contactPoint": {
"@type": "vcard:Contact",
"fn": "Your contact point",
"hasEmail": "mailto:[email protected]"
},
"programCode": [
"010:000"
],
"landingPage": "",
"title": "Initial field conditions at Kane\u2018ohe Bay, Oahu, Hawaii and abundances of Parvocalanus crassirostris and Bestilina similis nauplii, May\/June 2013 (EAGER: Copepod nauplii project) (NCEI Accession 0277882)",
"description": "This dataset contains biological, physical, and survey - biological data collected at lab UHawaii_SOEST during deployment Goetze_2012-2013 in the North Pacific Ocean from 2013-05-27 to 2013-06-05. These data include abundance, chlorophyll a, salinity calculated from CTD primary sensors, and water temperature. The instruments used to collect these data include Flow Meter, Microscope - Optical, Plankton Net, and qPCR Thermal Cycler. These data were collected by Erica Goetze of University of Hawaii at Manoa as part of the \"New molecular methods for studying copepod nauplii in the field (EAGER: Copepod nauplii)\" project. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) submitted these data to NCEI on 2021-01-20.\n\nThe following is the text of the dataset description provided by BCO-DMO:\n\nInitial conditions and naupliar abundances of Parvocalanus crassirostris and Bestilina similis: MEPS 2017\n\nDataset Description:\nAcquisition Description:\nFrom Jungbluth et al. 2017 \u2013 MEPS:\n\nEstimates of in situ naupliar abundance\n\nNaupliar abundances of the 2 target species in situ were estimated using a quantitative polymerase chain reaction (qPCR)-based method (Jungbluth et al. 2013), as well as microscopic counts of calanoid and cyclopoid nauplii. The qPCR-based method allows application of individual species grazing rates to in situ abundances to estimate the total potential grazing impact of each species. Samples were collected by duplicate vertical microplankton net tows (0.5 m diameter ring net, 63 \u00b5m mesh) from near bottom (10 m depth) to the surface with a low speed flow meter (General Oceanics). The contents of each net were split quantitatively. One half was size-fractionated through a series of 5 Nitex sieves (63, 75, 80, 100, and 123 \u00b5m) to separate size groups of nauplii from later developmental stages, and each was preserved in 95% non-denatured ethyl alcohol (EtOH). The second half of the sample was preserved immediately in 95% EtOH for counts of total calanoid and total cyclopoid nauplii, which were used for comparison to the qPCR-based results of the abundance of each calanoid species. All samples were stored on ice in the field until being transferred to a -20\u00b0C freezer in the laboratory. EtOH in the sample bottles was replaced with fresh EtOH within 12 to 24 h of collection to ensure high-quality DNA for analysis (Bucklin 2000).\n\nThe 3 smallest plankton size fractions from the net collection were analyzed with qPCR to enumerate P. crassirostris and B. similis nauplius abundances (Jungbluth et al. 2013). In brief, DNA was extracted from 3 plankton size fractions (63, 75, and 80 \u00b5m) using a modified QIAamp Mini Kit procedure (Qiagen). The total number of DNA copies in each sample was then measured using species-specific DNA primers and qPCR protocols (Jungbluth et al. 2013). On each qPCR plate, 4 to 5 standards spanning 4 to 5 orders of magnitude in DNA copy number were run along with the 2 biological replicates of a size fraction for each sampling date along with a no template control (NTC), all in triplicate. A range of 0.04 to 1 ng \u00b5l-1 of total DNA per sample was measured on each plate ensuring that the range of standards encompassed the amplification range of samples, with equal total DNA concentrations run in each well on individual plates. In all cases, amplification efficiencies ranged from 92 to 102%, and melt-curves indicated amplification of only the target species. The qPCR estimate of each species' mitochondrial cytochrome oxidase c subunit I (COI) DNA copy number was converted to an estimate of nauplius abundance using methods described in Jungbluth et al. (2013).\n\nConditions\n\nSalinity and temperature in the field were measured using a YSI 6600V2 sonde prior to collecting water for bottle incubations. For chl a, triplicate 305 ml samples were filtered onto GF\/Fs (Whatman), flash-frozen (LN2), and kept at -80\u00b0C freezer until measurements were made 4 mo later. Chl a (and phaeopigment) was measured using a Turner Designs (model 10AU) fluorometer, using the standard extraction and acidification technique (Yentsch & Menzel 1963, Strickland & Parsons 1972).\n\nFor complete methodology, see the Supplemental Files section.",
"language": "",
"distribution": [
{
"@type": "dcat:Distribution",
"mediaType": "application\/json",
"accessURL": "https:\/\/www.ncei.noaa.gov\/metadata\/geoportal\/\/rest\/metadata\/item\/gov.noaa.nodc%3A0277882"
},
{
"@type": "dcat:Distribution",
"mediaType": "text\/html",
"accessURL": "https:\/\/www.ncei.noaa.gov\/metadata\/geoportal\/\/rest\/metadata\/item\/gov.noaa.nodc%3A0277882\/html"
},
{
"@type": "dcat:Distribution",
"mediaType": "application\/xml",
"accessURL": "https:\/\/www.ncei.noaa.gov\/metadata\/geoportal\/\/rest\/metadata\/item\/gov.noaa.nodc%3A0277882\/xml"
},
{
"@type": "dcat:Distribution",
"mediaType": "application\/octet-stream",
"accessURL": "https:\/\/www.ncei.noaa.gov\/access\/metadata\/landing-page\/bin\/gfx?id=gov.noaa.nodc:0277882"
}
],
"bureauCode": [
"010:04"
],
"modified": "2023-05-05T11:47:48.134Z",
"publisher": {
"@type": "org:Organization",
"name": "Your Publisher"
},
"theme": "",
"keyword": [
"0277882",
"CHLOROPHYLL A",
"SALINITY",
"species abundance",
"WATER TEMPERATURE",
"flow meter",
"microscope",
"net - plankton net",
"biological",
"physical",
"survey - biological",
"University of Hawai'i at M\u0101noa",
"Biological and Chemical Oceanography Data Management Office",
"Kaneohe Bay",
"North Pacific Ocean",
"oceanography",
"BCO-DMO > Biological and Chemical Oceanography Data Management Office",
"New molecular methods for studying copepod nauplii in the field (EAGER: Copepod nauplii)",
"Goetze_2012-2013",
"Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1255697",
"abundance",
"chlorophyll a",
"experiment id",
"latitude",
"longitude",
"no standard parameter",
"salinity calculated from CTD primary sensors",
"water temperature",
"EARTH SCIENCE > OCEANS > OCEAN CHEMISTRY > CHLOROPHYLL",
"EARTH SCIENCE > OCEANS > OCEAN TEMPERATURE > WATER TEMPERATURE",
"EARTH SCIENCE > OCEANS > SALINITY\/DENSITY > SALINITY",
"chl_a",
"chl_std_err",
"counted_total_nauplii",
"counted_total_nauplii_se",
"date_local",
"experiment",
"lat",
"lon",
"qPCR_Bestiolina",
"qPCR_Bestiolina_se",
"qPCR_Parvocalanus",
"qPCR_Parvocalanus_se",
"sal",
"temp",
"Flow Meter",
"Microscope - Optical",
"Plankton Net",
"qPCR Thermal Cycler",
"MICROSCOPES > MICROSCOPES",
"PLANKTON NETS",
"General Oceanics Digital Flowmeter",
"Roche LC96 thermalcycler",
"microplankton net",
"unknown (Microscope - Optical)",
"lab UHawaii_SOEST",
"LABORATORY > LABORATORY",
"OCEAN > PACIFIC OCEAN > CENTRAL PACIFIC OCEAN > HAWAIIAN ISLANDS",
"OCEAN > PACIFIC OCEAN > NORTH PACIFIC OCEAN",
"Kaneohe Bay, HI",
"environment",
"oceans",
"biota"
]
}
